The present invention concerns the use of an xe2x80x9cimmunodeficiency-virus suppressing lymphokine (ISL)xe2x80x9d to inhibit the replication of viruses, therapeutic compositions containing ISL or nucleic acid molecules coding therefor.
ISL activity is defined by inhibition of HIV replication on primary lymphocytes (PBMC).
It is known that certain CD8+ cells, e.g., those of human and animal origin which, in addition to being CD8+ are HLA-DR+, CD28+, or CD11Bxe2x88x92, show activity in suppressing immunodeficiency viruses, such as HIV and SIV. This activity has been attributed to a molecule referred to as immunodeficiency virus suppressing lymphokine or xe2x80x9cISLxe2x80x9d. ISL is capable of inhibiting the replication of viruses in CD4+ cells that are infected with HIV or SIV (Ennen, Findeklee, Kurth et al (Proc. Natl. Acad. Sci. USA, Vol. 91, p. 7207-7211 (1994). However, the identity of ISL has to date been unclear. It has been known since at least 1989 (Walker, C. M., and Leighly, J. A., Immunology, Vol. 66, p. 628-630 (1989)) that there exists a soluble factor secreted by stimulated human CD8+ T lymphocytes that down-regulates HIV replication in CD4+ T cells. However, it has until now been impossible to establish whether this activity results from a single substance, and it has also until today even been impossible to isolate and characterize a substance with this activity although there exist a lot of publications in which methods of setting up corresponding cell cultures are described and methods of purifying such antiviral factors are suggested. Such publications are, e.g., WO 94/23058 and WO 93/0883 as well as by Mackewicz et al (Lancet, 344, p. 1671-1673 (1994)); Mackewicz et al (AIDS Research and Human Retroviruses, Vol. 8, No. 6, p. 1039-1050 (1992); Castro, Walker et al (Cellular Immunology 132, p. 246-255, (1991); Blackbourn et al (Journal of Medical Primatology No. 23, p. 343-354 (1994); Chen et al (AIDS Research and Human Retroviruses Vol. 9, No. 11, p. 1079-1086)); Kannagi et al (The Journal of Immunology, Vol. 140, No. 7, p. 2237-2242 (1988)); Joag et al (Virology 200, p. 436-446 (1994)); Walker, Moody et at (Science, Vol. 234, p. 1563-1566 (1986)); Walker, Erickson et al (Journal of Virology, Vol. 65, No. 11, p. 5921-5927 (1991)); Walker, Thomson-Honnebier et al (Cellular Immunology 137, p. 420-428 (1991)); Knuchel, Bednarik et al (Journal of Acquired Immune Deficiency Syndromes, No. 7, p. 438-446 (1994)); Ennen, Findeklee, Kurth et al (Proc. Natl. Acad. Sci. USA, Vol. 91, p. 7207-7211 (1994)) and Hsueh, Walker et al (Cellular Immunology 159, p. 271-279 (1994)).
In spite of the above-mentioned intensive investigation that has been carried out on the immunodeficiency virus-suppressing activities produced from CD8+ cells for about seven years, the biological nature (especially the molecular structure of ISL), apart from the assumption that ISL is a protein, is completely unclear. Also unclear are:
its gene or genes if it consists of several factors;
the way in which it acts on infected and non-infected CD4+ cells. There are preliminary indications that the action of ISL is based on a negative regulation of the transcription rate of HIV-LTR (long terminal repeat);
its mechanism of action in other infections. It may be assumed that viruses whose transcription is regulated by transcription factors that are comparable to those of HIV will also be subjected to a negative regulation by ISL;
its mechanism of action on normal and malignant cell proliferation. According to the present state of knowledge it cannot be ruled out that, similar to the interferons, an inhibitory effect on normal or malignant cell proliferation may be possible;
the fact whether ISL could regulate CD4 expression;
why in the case of HIV-infected patients a decrease in the ISL activity that is measurable in vitro occurs over time;
the fact whether ISL may also be partly responsible for the long latency period between infection and development of disease in humans infected with HIV, i.e., be positively correlated with a positive prognosis.
The problem has therefore arisen of identifying ISL and to clarify whether it represents one or several substances as well as to examine it with regard to its therapeutic action on immunodeficiency viruses and other viruses.
Cruikshank and Center (Journal of Immunology 128 (1982) 2569-2574) describe a protein called xe2x80x9clymphocyte chemoattractant factorxe2x80x9d (LCF), which has a sequence quite similar to the sequence of the polypeptides of the invention. It is expressed by human lymphocytes and is a member of the group of lymphokines. After appropriate purification by gel filtration a homogeneous product was obtained with a molecular weight of approximately 56,200 which is cleaved by sodium dodecyl sulphate into monomers with a molecular weight of ca. 14,400. It was assumed that this lymphokine played a role in the formation and amplification of the delayed type of immune response (delayed type hypersensitivity reaction).
The nucleic acid sequence of LCF is described by Cruikshank, W., et al., Proc. Nat. Acad. Sci. USA 91 (1994) 5109-5113. The nucleotide sequence and the protein sequence derived therefrom are available under Accession Number M90391 at GenBank data base and are shown in SEQ ID NO:3 and SEQ ID NO:4.
From Cruikshank et al (Journal of Immunology 138, 3817-3823 (1987)) it is also known that LCF stimulates the expression of interleukin 2 (IL2) receptors and HLA-DR antigens on CD4+ lymphocytes. LCF is therefore also referred to as growth factor. Furthermore Cruikshank et al described in the Journal of Immunology 146, 2928-2934 (1991) that LCF induces CD4-dependent intracytoplasmic signals in lymphocytes and thus concluded that these signals act as a second type of messengers. In the J. Exp. Med. 173, p. 1521-1528 (1991) Rand, Cruikshank et al additionally describe the stimulation of human eosinophils by LCF and its massive production by activated T-lymphocytes. Finally in Proc. Natl. Acad. Sci. USA, Vol. 91, p. 5109-5113 (1994) Cruikshank et al described a cloning of LCF by isolating the LCF cDNA from an expression library from mitogen-stimulated mononuclear blood cells (PBMC: peripheral blood mononuclear cells) and introduction into E. coli to produce biologically active recombinant LCF protein (rLCF). Recombinant LCF shows an isoelectric point of 9.0 (Center, D. M., et al., J. Lab. Clin. Med. 125 (1995) 167-171).
Cruikshank, W., et al. (Proc. Nat. Acad. Sci. USA 91 (1994) 5109-5113) describes that LCF may contribute to recruitment of eosinophils and CD4+ mononucleic cells concomitantly in intracellular reactions. Cruikshank further suggests that LCF activity on CD4+ cells would provide a mechanism for the accumulation of non-sensitized T cells in tissue. Its ability to prime CD4+ T cells for IL-2 responsiveness might play a role in the specific expansion of this T cell population. In WO 94/28134 the same authors suggest to use LCF as an immunosuppressive agent or as part of an immunosuppressive therapy. However, an antiviral activity of LCF was neither described in nor obvious from these publications. To the contrary, Center, D. M., et al., (1995) (supra) conclude that LCF does amplify the inflammatory process.
The subject-matter of the invention is the identification and molecular cloning of an immuno-deficiency-virus suppressing lymphokine (ISL) and the isolation of nucleic acid molecules which encode polypeptides with ISL activity. Such polypeptides have improved properties, especially a higher activity than the polypeptide described in WO 94/28134. More specifically, the invention relates to those nucleic acid molecules which encode eukaryotic ISL, including human, monkey and other species. Specifically preferred are nucleic acid molecules which hybridize to SEQ ID NO:1 under stringent conditions as set forth below and code for a polypeptide with ISL activity. It can be shown that natural, synthetic, and recombinantly produced ISL is able to suppress the replication of viruses, especially of retroviruses, in vivo and in vitro.
The nucleotide sequences according to the invention encode a polypeptide that binds to CD4+ lymphocytes and can suppress the replication of viruses such as, in particular, HIV-1, HIV-2 and SIV strains. Therefore, such polypeptides, active fragments and derivatives also are a subject-matter of the present invention. The function of ISL is not limited by its presentation in an MHC complex.
A further subject-matter of the invention is the use of ISL for the therapeutic treatment of viral infections, preferably retroviral infections and/or viral-based benign and malignant diseases, and its use for the production of a therapeutic composition containing ISL, as well as its use for the manufacture of such therapeutic agents.
A further subject-matter of the invention is a therapeutic composition containing ISL in an amount effective for treatment of such diseases, especially viral infections. The pharmaceutical composition or agent also contains suitable pharmaceutically compatible carrier substances.
A further subject-matter of the invention is a polyclonal or monclonal anti-ISL antibody or an immuno-active fragment thereof, as well as methods for producing such antibodies and their use for ISL determination and detection of viral infections of eukaryotic cells, especially mammalian samples, preferably derived from mammalian cells.
Another subject-matter of the invention is the use of ISL for the detection of virus-activated mammalian cells, especially T cells.
A further subject-matter of the invention is a method for the determination of soluble or insoluble, free or cell-bound ISL. Such a diagnostic method can be used for the detection of acute or chronic infections, for monitoring the course of viral infections and/or for the monitoring and detection of viral-based benign and malignant diseases.
A further subject-matter of the invention is the use of a nucleotide molecule which can secure expression of ISL in a eukaryotic cell for the activation of ISL in human cells, for in vivo or ex vivo gene therapy.
Another subject-matter of the invention is a therapeutic composition useful in treating a pathological condition characterized by viral replication, especially retroviral replication, comprising at least a substance which activates ISL activity in CD8+ T cells, and a pharmaceutically acceptable carrier.
Therefore, a further subject-matter of the invention is a method for the production of a substance and a therapeutic agent for inhibition of the replication of viruses in a patient, said method comprising combining with a pharmaceutically acceptable carrier a therapeutically effective amount of a substance which activates expression of a protein with ISL activity, preferably of a protein with the amino acid sequence shown in SEQ ID NO:2 in CD8+ T cells, in vivo and in vitro, to such an extent that viral replication in CD4+ cells is inhibited.
A further subject-matter of the invention is a therapeutic composition useful in treating a pathological condition characterized by viral replication, especially retroviral replication, comprising at least a substance which activates ISL activity in CD8+ T cells, and a pharmaceutically acceptable carrier.
The invention is based on new isolated polypeptides with ISL activity which inhibit the replication of HIV-1, preferably HIV-1SF2 in CD8+-depleted peripheral blood lymphocytes (PBMC) which are prepared from buffy coat of non-retrovirally infected normal human blood samples in an assay (also referred to in the following as an HIV inhibition assay),
a) whereby said CD8+-depleted PBMC are incubated with 0.1 xcexcg of said polypeptide/1.5xc3x97106 cells in 150 xcexcl medium for half an hour at 37xc2x0 C.;
b) said CD8+-depleted PBMC are subsequently infected with HIV-1, preferably with HIV-1SF2 by incubating 1.5xc3x97106 cells in 150 xcexcl with 50 xcexcl HIV-1 stock solution containing 50 tissue infectious doses 50 (TCID50) for 1 h at 37xc2x0 C.;
c) said infected CD8+-depleted PBMC are washed to remove unbound HIV-1 and, preferably, polypeptide;
d) CD8+-depleted PBMC are cultivated at 37xc2x0 C. in a 5% CO2 atmosphere and medium is changed and said polypeptide is added after 3, 6, 9, and 12 days;
e) the amount of HIV-1 in the CD8+-depleted PBMC cell culture supernatants is determined at days 9 and 12 post infection by serially threefold dilutions of supernatant and inoculation in quadruplicate wells onto 2000 cells in 150 xcexcl medium of a highly susceptible indicator cell line, which must be routinely infectable to an extent of 85% or greater with said HIV-1 strains, preferably the human HTLV-transformed lymphoma cell line MT4;
f) virus replication in each well is determined 8 days post infection by determination of the reverse transcriptase (RT) in the cell culture supernatant (there is preferably applied the Reverse Transcriptase Assay of Boehringer Mannheim GmbH, Biochemica, 68298 Mannheim, Germany, Order No.: 1468 120) of every single well following the instructions of the manufacturer);
g) the tissue culture infectious doses 50 (TCID50) of the CD8+-depleted PBMC cultures is calculated preferably following the method published by Karber (Karber, G. 1931. Assay for statistical analysis of pharmacological experiments. Arch. Exper. Path. V. Pharmakol. 162, 148) according to the formula:
log TCID50=Lxe2x88x92d(sxe2x88x920.5),
wherein
L=log of the lowest virus dilution
d=log of virus dilution
s=sum of virus-positive cell cultures;
h) inhibition of HIV-1 replication in the CD8+-depleted PBMC cultures is calculated by comparison of virus content of cell culture supernatants in an assay according to steps a) to g) and the virus content of an assay according to steps a) to g) where said polypeptide to be tested for inhibition of HIV replication is replaced by buffer without polypeptide (untreated control);
i) inhibition is found if the amount of viral replication in CD8+-depleted PBMC is inhibited in such a way that the amount of virus is about 50% or less, more preferably 10% or less, most preferably 1% or less in comparison to the untreated control,
and the polypeptide
i) is coded by the DNA sequence shown in SEQ ID NO:1 or a sequence complementary to the sequence shown in SEQ ID NO:1,
ii) is coded by a DNA sequence which hybridizes with SEQ ID NO:1 or SEQ ID NO:3 or which hybridizes with a DNA sequence complementary to SEQ ID NO:1 or SEQ ID NO:3, under stringent conditions,
iii) is coded by DNA sequences which, if there was no degeneracy of the genetic code, would hybridize under stringent conditions with the sequences defined in i) or ii),
with the proviso that the polypeptide differs from the polypeptide coded by the DNA sequence shown in SEQ ID NO:3.
Useful polypeptides with ISL activity besides the preferred polypeptides of SEQ ID NO:2 or SEQ ID NO:4 are, for example, the also preferred polypeptides of FIG. 3. FIG. 3 also shows DNA sequences which code for these polypeptides. A further preferred polypeptide is a polypeptide according to the invention wherein amino acid 26 (alanine) is deleted. Such a polypeptide also exists as natural allelic forms in humans and monkeys.
In the examples which follow, a strain of HIV-1 known as HIV-1SF2 is used. This is a typical North American/European strain. Its nucleotide sequence is set forth in SEQ ID NO:7, and is also accessible via GenBank Accession Number K02007. Other HIV strains include HIV-1SF33 (SEQ ID NO:8), as well as strains set forth in, e.g., Cheng-Mayer et al., J. Virol 64 (1990) 4390-4398; Levy, J. A., et al., Science 232 (1986) 998-1001; Luciw, P. A., et al., Nature 312 (1984) 760-763; Sanchez-Pescador, R., et al., Science 227 (1985) 484-492.
In the assay applied for determination of ISL activity, Ficoll gradient purified and phytohaemagglutinin (PHA) stimulated PBMC were infected with an HIV-1 strain and cultivated. CD8+-depleted PBMC are used because of improved accuracy compared to the use of PBMC. However, it is also possible to use PBMC. CD8+-depleted cells are selected by cell sorting using specific antibodies. Such methods are widely known state of the art. The culture supernatants are tested for their virus content. For this purpose, e.g., determination of the reverse transcriptase or P24 antigen can be carried out. Another possibility is to determine the level of infection of highly susceptible indicator cell lines, referred to a virus-free cell supernatant in each case. In such a test, ISL activity will be found if the substance to be tested causes a reduction of reverse transcriptase activity for at least about 50%, preferably 70%, more preferably 90%, or more.
The polypeptide can be defined by its DNA sequence and by the amino acid sequence derived therefrom. The ISL polypeptide can occur in natural allelic variations which differ from individual to individual. Such variations of the amino acids are usually amino acid substitutions. However, they may also be deletions, insertions or additions of amino acids to the total sequence. The ISL protein according to the inventionxe2x80x94depending, both in respect of the extent and type, on the cell and cell type in which it is expressedxe2x80x94can be in glycosylated or non-glycosylated form. Polypeptides with ISL activity can easily be identified by the above-described HIV inhibition assay.
FIG. 3 shows a comparison of the DNA and polypeptide sequences of human and different monkey ISL. It was found furthermore that an allelic variant wherein codon 26 (coding for Ala) is deleted exists in all of these species. As can be seen from FIG. 3, ISL polypeptides and nucleic sequences coding therefor, wherein amino acid 7 is Ser or Thr, amino acid 25 is Thr or Ser, amino acid 31 is Cys or Tyr, amino acid 76 is Val or Ile, amino acid 86 is Gly or Ala, amino acid 112 is Ile or Thr, amino acid 121 is Ser or Pro and/or amino acid 128 is Gly or Ala, are preferred. There are also preferred polypeptides in which amino acid 26 is deleted. Such variations can improve the antiviral tumor therapeutic (benign or malignant) and/or immunosuppressive activity of ISL without changing the biological properties in general.
xe2x80x9cPolypeptide with ISL activity or ISLxe2x80x9d means also proteins with minor amino acid variations but with substantially the same ISL activity. Substantially the same means that the activities are of the same biological properties and the polypeptides show preferably at least 75% homology in amino acid sequence. More preferably, the amino acid sequences are at least 90% identical.
xe2x80x9cIndicator cell linexe2x80x9d means as lymphoma cell line which must be routinely infectable to an extent of 85% or greater with the HIV-1 strain which is used in the HIV inhibition assay. Preferably, such an indicator cell line is MT4 which is described in Norley, S. G., et al, Biologicals 21 (1993) 251-258 which is incorporated herein by reference. Other useful lymphoma cell lines are described by Cheng-Mayer, C., et al, Virol. 181 (1991) 288-294 and J. Virol. 65 (1991) 6931-6941 which also are incorporated herein by reference. In these publications there are described lymphoma cell lines which are infectable by HIV-1 to a greater or lesser extent. From the named cell lines only those cell lines which are routinely injectable to an extent of 85% or greater with the HIV strain of the HIV inhibition assay are useful.
xe2x80x9cISL activityxe2x80x9d denotes the anti-viral action of the tissue culture supernatant of activated and non-activated CD8+ lymphocytes of human (ISL) or animal origin (e.g. ISL in the lymphocytes of African green monkeys (ISL-agm)).
xe2x80x9cISLxe2x80x9d preferably denotes the molecule whose sequence is shown in SEQ ID NO:1, 2, 3, or 4.
ISL is a polypeptide which is active in its glycosylated or unglycosylated form. The unglycosylated form can be produced by recombinant technology in prokaryotic cells.
ISL is produced by non-activated (small amount) as well as by activated T lymphocytes. ISL binds to CD4+ lymphocytes, preferably to the CD4 receptor molecule or to a molecule associated with the CD4 molecule. ISL has suppressed the replication of all HIV-1 and HIV-2 strains tested up to now as well as all previously tested SIV strains. This effect can be observed on CD4+-lymphocytes from peripheral blood as well as in a number of human CD4+-positive T cell lymphomas. ISL has an interspecies-specific action since at least the ISL of the African green monkey is capable of suppressing the replication of HIV in human CD4+ cells. The function of ISL is not limited by an incompatibility of the MHC locus (major histocompatibility complex) and it does not have a lytic action on cells. ISL is synthesized by the CD8+ lymphocytes of asymptomatic patients infected with HIV and less by cells from symptomatic patients. ISL is also produced by activated CD8+ cells of healthy blood donors. The extent of ISL synthesis correlates quantitatively with the clinical status of HIV-infected patients. The ISL activity in asymptomatic HIV patients is higher (with a comparable number of activated CD8+ lymphocytes) than in symptomatic patients. The antiviral action of ISL is not identical with previously known lymphokines and interferons. ISL activity has also been detected in the cell culture supernatant of activated CD8+ lymphocytes of HIV-infected and non-infected chimpanzees as well as of SIV-infected and non-infected African green monkeys, Rhesus monkeys and Sooty mangabees (Ennen, J., et al, Proc. Natl. Acad. Sci. USA 91 (1994) 7207-7211). ISL may be capable of protecting against superinfections with other HIV/SIV strains (Cheng-Mayer, C., et al, J. Virol. 64 (1990) 4390-4398).
A protein with ISL activity is described in Cruikshank et al, Proc. Natl. Acad. Sci. USA 91 (1994) 5109-5113 and WO 94/28134 and is named LCF (see supra). This protein is coded by SEQ ID NO:3 and therefore has the sequence SEQ ID NO:4. Cruikshank refers, for the sequence reported to Accession Number M90391 accorded by GenBank data base. Whereas the protein sequences shown in GenBank and FIG. 2 of Cruikshank are identical, the nucleic acid sequences exhibit a difference in nucleotide 1070. Whereas in the GenBank sequence this nucleotide is T, in FIG. 2 of Cruikshank""s publications this nucleotide is G. As TTG does not code for Phe but for Leu, it is clear that G is a typographical error. This is confirmed by cloning of ISL cDNA derived from independent PCR amplifications. From these clones it is clear that the LCF sequence in codon 96 is indeed represented by the sequence TTT. Therefore, nucleotide 1070 clearly is T.
The term xe2x80x9cnucleic acid moleculexe2x80x9d denotes a polynucleotide which can be, for example, a DNA, RNA, or derivatized active DNA or RNA. DNA and/or RNA molecules are preferred, however.
The term xe2x80x9chybridize under stringent conditionsxe2x80x9d means that two nucleic acid fragments are capable of hybridization to one another under standard hybridization conditions described in Sambrook et al., xe2x80x9cExpression of cloned genes in E. colixe2x80x9d in Molecular Cloning: A laboratory manual (1989) Cold Spring Harbor Laboratory Press, New York, USA, 9.47-9.62 and 11.45-11.61.
More specifically, xe2x80x9cstringent conditionsxe2x80x9d as used herein refer to hybridization in 6.0xc3x97SSC at about 45xc2x0 C., followed by a wash of 2.0xc3x97SSC at 50xc2x0 C. For selection of the stringency the salt concentration in the wash step can be selected, for example from about 2.0xc3x97SSC at 50xc2x0 C., for low stringency, to about 0.2xc3x97SSC at 50xc2x0 C., for high stringency. In addition, the temperature in the wash step can be increased from low stringency conditions at room temperatures, about 22xc2x0 C., to high stringency conditions at about 65xc2x0 C.
The term xe2x80x9cisolatedxe2x80x9d as used throughout this application refers to a nucleic acid or polypeptide having an ISL activity and is substantially free of cellular material or culture medium, when produced by recombinant DNA techniques, or chemical precursors or other chemicals, when synthesized chemically. An isolated nucleic acid is preferably free of sequences which naturally flank the nucleic acid (i.e. sequences located at the 5xe2x80x2 and the 3xe2x80x2 ends of the nucleic acid) in the organism from which the nucleic acid is derived.
ISL can be isolated and purified from activated T cells by affinity chromatography using a monoclonal antibody against ISL. It is also preferred to use other known protein purification techniques, including immunoprecipitation, gel filtration, ion exchange chromatography, chromatofocussing, isoelectric focussing, selective precipitation, electrophoresis, and the like. Fraction isolated during purification procedures can be analyzed for the presence of ISL activity by using ISL specific antibodies.
The polypeptides according to the invention can also be produced by recombinant means, or synthetically. Non-glycosylated ISL polypeptide is obtained when it is produced recombinantly in prokaryotes. With the aid of the nucleic acid sequences provided by the invention it is possible to search for the ISL gene or its variants in genomes of any desired cells (e.g. apart from human cells, also in cells of other mammals), to identify these and to isolate the desired gene coding for the ISL protein. Such processes and suitable hybridization conditions are known to a person skilled in the art and are described, for example, by Sambrook, J., et al., xe2x80x9cExpression of cloned genes in E. colixe2x80x9d in Molecular Cloning: A laboratory manual (1989) Cold Spring Harbor Laboratory Press, New York, USA, and B. D. Hames, S. G. Higgins, Nucleic acid hybridisationxe2x80x94a practical approach (1985) IRL Press, Oxford, England. In this case the standard protocols described in these publications are usually used for the experiments.
The use of recombinant DNA technology and the knowledge of the HIV inhibition assay enables the production of numerous active ISL derivatives. Such derivatives can, for example, be modified in individual or several amino acids by substitution, deletion or addition. The derivatization can, for example, be carried out by means of site directed mutagenesis. Such variations can be easily carried out by a person skilled in the art (J. Sambrook, B. D. Hames, loc. cit.). It merely has to be ensured by means of the above-mentioned HIV inhibition assay that the characteristic properties of ISL (inhibition of virus replication) are preserved. The invention therefore in addition concerns an ISL polypeptide which is a product of a prokaryotic or eukaryotic expression of an exogenous DNA.
The invention further concerns an isolated nucleic acid molecule which codes for a polypeptide or active fragment or derivative thereof, which inhibits the replication of HIV-1 in CD8+-depleted PBMC, said PBMC being prepared from buffy coat of non-retrovirally infected normal human blood samples, in the above-mentioned HIV inhibition assay, and wherein said nucleic acid molecule is selected from the group of
i) a DNA molecule as shown in SEQ ID NO:1 or a sequence complementary to the sequence shown in SEQ ID NO:1,
ii) nucleic acid molecules which hybridize with SEQ ID NO:1 or SEQ ID NO:3 or which hybridize with a DNA sequence complementary to SEQ ID NO:1 or SEQ ID NO:3, under stringent conditions,
iii) nucleic acid molecules which, if there was no degeneracy of the genetic code, would hybridize under stringent conditions with the sequences defined in i) or ii),
with the proviso that said isolated nucleic acid molecule is not identical with SEQ ID NO:3.
In a preferred embodiment of the invention, also nucleic acid molecules are disclaimed which code for a polypeptide of SEQ ID NO:4.
With the aid of such nucleic acids coding for an ISL protein, the protein according to the invention can be obtained in a reproducible manner and in large amounts. For expression in prokaryotic or eukaryotic organisms, such as prokaryotic host cells or eukaryotic host cells, the nucleic acid is integrated into suitable expression vectors, according to methods familiar to a person skilled in the art. Such an expression vector preferably contains a regulatable/inducible promoter. These recombinant vectors are then introduced for the expression into suitable host cells such as, e.g., E. coli as a prokaryotic host cell or. Saccharomyces cerevisiae, Terato carcinoma cell line PA-1 sc 9117 (Bxc3xcttner et al., Mol. Cell. Biol. 11 (1991) 3573-3583), insect cells, CHO or COS cells as eukaryotic host cells and the transformed or transduced host cells are cultured under conditions which allow an expression of the heterologous gene. The isolation of the protein can be carried out according to known methods from the host cell or from the culture supernatant of the host cell. Such methods are described for example by Ausubel I., Frederick M., Current Protocols in Mol. Biol. (1992), John Wiley and Sons, New York. Also in vitro reactivation of the protein may be necessary if it is not found in soluble form in the cell culture.
The detection of transformed or transduced host cells which recombinantly produce the ISL protein and the purification of the protein are preferably carried out by means of antibodies which bind to this protein. Such antibodies can be obtained in a simple manner according to known methods by using the protein according to the invention as an antigen or an immunogen.
The invention therefore in addition concerns the use of the protein with ISL activity according to the invention for the production of antibodies which bind to this protein.
Anti-ISL antibodies are produced by immunization and appropriate vertebrate host with purified ISL or polypeptide derivatives of ISL, preferably with an adjuvant. Said techniques are well-known in the literature and are described, for example, by Harlow and Lane eds., Antibodies: A laboratory manual (1988), Cold Spring Harbor Laboratories Press.
For this, animals which are usually used for this purpose, such as, in particular, sheep, rabbits or mice, are immunized with the protein according to the invention (preferably with the protein of FIG. 3), and subsequently the antiserum is isolated from the immunized animals according to known methods or spleen cells of the immunized animals are fused with immortalized cells, such as e.g. myeloma cells, according to the method of Kxc3x6hler and Milstein (Nature 256 (1975) 495-497). Those cells which produce a monoclonal antibody against the ISL protein are selected from the hybridoma cells obtained in this way and cloned. The monoclonal or polyclonal antibodies obtained in this way can be bound to a support material, such as e.g. cellulose, for an immunoabsorptive purification of ISL. Furthermore, antibodies of this kind can be used for the detection of ISL in samples, such as e.g. cut tissue or body fluids, preferably for the determination of viral infections and virally induced benign and malignant diseases, most preferably for the determination of retroviral infections in mammalian samples. In such assays ISL is bound immunologically to its antibody in the specific step. The invention therefore additionally concerns specific antibodies against the ISL protein preferably the ISL proteins not disclosed by Cruikshank, which are obtainable by immunizing an animal with said ISL protein and isolating the antibodies from the serum or spleen cells of the immunized animals, and their use for the determination of ISL.
The invention in addition concerns the use of a polypeptide defined in the above-mentioned manner including a protein of SEQ ID NO:3, for the production of a pharmaceutical agent and for the treatment of viral infections, preferably retroviral infections such as HIV infections, and for use in therapy of benign and malignant diseases, especially in tumor therapy, most preferably for the treatment of viral-induced tumors.
The protein is processed, if desired together with the usually used auxiliary agents, fillers and/or additives, in a pharmaceutical formulation for the said therapeutic applications.
The invention therefore in addition concerns a therapeutic composition containing a ISL polypeptide according to the invention and if desired together with the auxiliary agents, fillers and/or additives that are usually used.
When the polypeptides according to the invention are applied for therapeutic use, their doses depend on the intended use. To find out the dose and optimize the application, usually such properties of the polypeptide as the half-life and bioavailability and the patient""s age and weight will also be taken into account. Optimum therapeutic effectiveness is achieved when the polypeptides according to the invention are applied as soon alter the infection as possible, preferably as soon after the first virus peak as possible. Here it is important that a concentration of the polypeptides and substances according to the invention which effectively inhibits virus replication is retained in the blood during the early stage of viral infection. This can be accomplished, for example, by the application of 1 to 1000 xcexcg/patient of the polypeptide according to the invention at 12 to 72 h-intervals. The period of application can be determined, suitably, by the method of determination of virus replication or virus quantity according to the invention or by other methods of virus determinations known to those skilled in the art. The application period may be in the range of from a few days to a few months.
The invention further concerns the use of the ISL genes or fragments thereof, preferably nucleic acid molecules coding for a polypeptide having ISL activity, or activating polynucleotides from the 5xe2x80x2 untranslated region, in gene therapy, and in particular, for the production of medicaments for gene therapy, preferably for an antiviral or immunosuppressive therapy, or a therapy of benign or malignant diseases.
Gene therapy of somatic cells can be accomplished by using, e.g., retroviral vectors, other viral vectors, or by non-viral gene transfer (for clarity cf. T. Friedmann, Science 244 (1989) 1275; Morgan 1993, RAC DATA MANAGEMET REPORT, June 1993).
Vector systems suitable for gene therapy are, for instance, retroviruses (Mulligan, R. C. (1991) in Nobel Symposium 8: Ethiology of human disease at the DNA level (Lindsten, J. and Pattersun Editors) 143-189, Raven Press), adeno associated virus (McLughlin, J. Virol. 62 (1988), 1963), vaccinia virus (Moss et al., Ann. Rev. Immunol. 5 (1987) 305), bovine papilloma virus (Rasmussen et al., Methods Enzymol. 139 (1987) 642) or viruses from the group of the herpes viruses such as Epstein Barr virus (Margolskee et al., Mol. Cell. Biol. 8 (1988) 2937) or herpes simplex virus.
There are also known non-viral delivery systems. For this, usually xe2x80x9cnudexe2x80x9d nucleic acid, preferably DNA, is used, or nucleic acid together with an auxiliary agent, such as, e.g., transfer reagents (liposomes, dendromers, polylysine-transferrine-conjugates (Feigner et al., Proc. Natl. Acad. Sci. USA 84 (1987) 7413).
There is particularly preferred an ex vivo gene therapy as described, e.g., in W. F. Anderson et al., U.S. Pat. No. 5,399,346. According to this method a polypeptide according to the invention is provided to a human by introducing human cells into a human, said human cells having been treated in vitro to insert therein a DNA segment encoding a polypeptide according to the invention, said human cells expressing in vivo in said human a therapeutically effective amount of said polypeptide. As human cells there are used preferably fibroblasts or autologous hematopoietic stem cells which are characterized preferably by CD3+, CD4xe2x88x92, CD8xe2x88x92. Primitive human hematopoietic progenitor cells, which are characterized by a high expression of CD34 and the absence of CD38 expression, are particularly preferred. However, also more differentiated hematopoietic stem cells such as CD34+ and CD38+ cells can be used. Such cells are described, e.g., by Terstappen et al., Blood 77 (1991) 1218 or Huang and Terstappen, Nature 360 (1992) 745. For the transfection of fibroblasts it is preferred to use cytomegalovirus (CMV)-based vectors. For the transfection of hematopoietic stem cells it is preferred to use retroviral vectors based on the molony murine leukemia vector (MMLV). Such techniques are described in the state of the art, e.g., in the above-mentioned U.S. Pat. No. 5,399,346 which is incorporated herein by reference. For the regulation of the therapeutic application, the use of a suicide gene system (e.g., tk-Gen (Ganciclovir)) is preferred.
Another preferred method of gene therapy is based on homologous recombination. In this, either the gene coding for the ISL protein can be inserted in one or more copies into the genome of somatic cells and/or the ISL gene endogenously present in the cells can be modulated, preferably activated.
Methods of homologous recombination are described, e.g., in Kucherlapati, Proc. in Nucl. Acids Res. and Mol. Biol. 36 (1989) 301; Thomas et al., Cell 44 (1986) 419-428; Thomas and Capecchi, Cell 51 (1987) 503-512; Doetschman et al., Proc. Natl. Acad. Sci. USA 85 (1988) 8583-8587 and Doetschman et al., Nature 330 (1987) 576-578. In these methods, a portion of DNA to be integrated at a specific site in the genome (gene fragment of ISL) is bound to a targeting DNA. The targeting DNA is a DNA which is complementary, (homologous) to a region (preferably within or proximal to the ISL gene) of the genomic DNA. When two homologous portions of a single-stranded DNA (e.g. the targeting DNA and the genomic DNA) are in close proximity to one another they will hybridize and form a double-stranded helix. Then the ISL gene fragment and the targeting DNA can be integrated into the genome by means of occurrence of recombination. This homologous recombination can be carried out both in vitro and in vivo (in the patient).
Preferably, there is used a DNA which codes for a protein having ISL activity, a fragment which inhibits ISL expression (knock-out sequence) or a fragment capable of activating, after integration of the genome of a cell, expression, in this cell, of a protein having ISL activity. Such a fragment may be, for example, a promoter and/or enhancer region which is heterologous to the corresponding ISL region or which, after integration into the ISL gene, activates the actually silent or to a little extent expressed ISL gene transcriptionally and/or translationally.
Thus, by means of this DNA, one or more ISL genes are newly introduced into the target cell, or the essentially transcriptionally silent gene in the genome of a mammalian cell is activated in such fashion that the mammalian cell is enabled to produce endogenous ISL protein. To this end, a DNA construct is inserted into the genome by homologous recombination, the DNA construct comprising the following: a DNA regulatory element capable of stimulating expression of this gene if operatively linked thereto; and one or more DNA target segments which are homologous to a region in this genome, which region is within or proximal to this gene. This construct is inserted into the genome of the mammalian cell in such fashion that the regulatory segment is operatively linked to the gene which codes for the protein having ISL, activity. Preferably, the construct further comprises amplifying sequences, especially if genes coding for proteins with ISL activity are inserted into the cell.
For the introduction of ISL genes into the target cells, the construct comprises a regulatory element, one or more ISL genes and one or more target segments. The target segments are chosen in such a way that they hybridize with an appropriate region of the genome, whereby, after homologous recombination, the inserted exogenous ISL genes are expressed.
There are known a large number of processes by which homologous recombination can be initiated. Preferably, homologous recombination takes place during DNA replication or mitosis of the cells. A DNA of this kind can be used for the production of an agent for therapeutic treatment of tumors and viral infection or for the production of homologous or heterologous ISL protein in a host organism.
A further subject-matter of the invention is a method for the determination of ISL polypeptides, nucleic acid sequences, virus-activated cells and ISL expression, preferably in samples of the human body such as human cell preparations, cell supernatants and body fluids such as blood, serum or plasma. Such a determination is useful for the detection of a viral infection, preferably of a mammalian, especially human, cell population. This method is particularly useful for the determination of the activation state of said cells and for the determination of a viral, preferably retroviral, infection of CD4+ cells. The diagnostic method is preferably applied immediately or as soon as possible after the first virus peak.
A further subject-matter of the invention is the use of an antibody which binds immunologically to a polypeptide which is obtainable by immunizing an animal with an ISL, polypeptide and isolating the antibodies from the serum or spleen cells of the immunized animals, for the determination of the ratio of activated/non-activated CD8+ and/or CD4+ cells in body fluids, especially in blood, serum or plasma.
Such tests can be provided on the basis of antibodies which are directed against part or all of ISL polypeptides. Such antibodies can be polyclonal or monoclonal antibodies, chimeric antibodies, humanized antibodies or fragments thereof such as F(ab), F(ab)2, single chain Fv, or the like. In such an assay, the antibodies are used for immuno-specific recognition of ISL. The further detection (with and without separation of this complex, and subsequent monitoring) can be done by the immuno-assays which are widely known in the state of the art. For instance, the antibody can be labelled by a monitoring agent such as a fluorescence indicator, radio-active or enzymatic labelling.
There is particularly preferred a diagnostic determination of ISL concentrations in serum and other body fluids as well as the number of ISL-producing cells, e.g., for the detection of acute or chronic infections (e.g. even in blood donors) or for monitoring the course of ((retro)viral) infections (e.g. in patients suffering from AIDS), wherein antibodies that are provided with a fluorescent indicated or a radioactive or enzymatic label or with a labelled anti-antibody are reacted, brought into contact with ISL or ISL-producing cells, the antigen/antibody complexes are separated in a known manner and their concentration is determined via the label.
A suitable test method comprises the steps of incubating CD8+ T cells, in vitro, with the substance to be tested and determining ISL activity, preferably after 1 to 12 days, by detecting ISL expression according to the invention or by determining ISL polypeptide, preferably by means of an anti-ISL-antibody-based test. Such a test is carried out, for example, in the following manner:
a) commercially available 96-well ELISA plates are coated with monoclonal anti-ISL-antibodies;
b) the sample to be tested for ISL content is added to an antibody coated well for 1 h at room temperature and the well is washed;
c) bound ISL is detected by incubation of an affinity purified polyclonal Goat-anti-ISL-IgG-Preparation followed by an anti-Goat specific horse radish peroxidase labelled antibody and subsequent visualisation with OPD.
Other immunological assays based on the state of the art are also suitable.
It is also possible to provide a test on the basis of the nucleic acid sequences of the ISL protein provided by the invention which can be used to detect nucleic acids preferably RNAS, most preferably mRNAS which code for ISL proteins. Such a test can for example be carried out in cells or cell lysates and by means of nucleic acid diagnostics. In this case the sample to be examined is brought into contact with a probe which would hybridize with the nucleic acid sequence coding for the ISL protein. A hybridization between the probe and nucleic acids from the sample indicates the presence of expressed ISL proteins. Such methods are known to a person skilled in the art and are for example described in WO 89/06698, EP-A 0 200 362, U.S. Pat. No. 2,915,082, EP-A 0 063 879, EP-A0 173 251, EP-A 0 128 018. In a preferred embodiment of the invention, the nucleic acid of the sample which codes for an ISL protein is amplified before testing, e.g. by the well-known PCR technique. A derivatized (labelled) nucleic acid probe is usually used in the field of nucleic acid diagnostics. This probe is brought into contact with a carrier-bound denatured DNA or RNA from the sample and in this process the temperature, ionic strength, pH value and other buffer conditions are selected in such a way thatxe2x80x94depending on the length of the nucleic acid sample and the resulting melting temperature of the expected hybridxe2x80x94the labelled DNA or RNA can bind to homologous DNA or RNA (hybridization, see also Southern, E. M., J. Mol. Biol. 98 (1975), 503-517; Wahl, G. M. et al., Proc. Natl. Acad. Sci. USA 76 (1979), 3683-3687). Suitable carriers are membranes or carrier materials based on nitrocellulose (e.g. Schleicher and Schxc3xcll, BA 85, Amersham Hybond, C.), reinforced or bound nitrocellulose in a powder form or nylon membranes derivatized with various functional groups (e.g. nitro group) (e.g. Schleicher and Schxc3xcll, Nytran; NEN, Gene Screen; Amersham Hybond M.; Pall Biodyne).
The hybridized DNA or RNA is then detected by incubating the carrier, after thorough washing and saturation to prevent unspecific binding, with an antibody or antibody fragment. The antibody or antibody fragment is directed towards the substance incorporated into the nucleic acid probe during the derivatization. The antibody is in turn labelled. It is, however, also possible to use a directly labelled DNA. After incubation with the antibodies, it is washed again in order to only detect specifically bound antibody conjugates. The determination is then carried out via the label of the antibody or antibody fragment according to well-known methods.
The detection of the ISL expression can be carried out, for example
as an in situ hybridization with immobilized whole cells using immobilized tissue smears and isolated metaphase chromosomes,
as a colony hybridization (cells) and plaque hybridization (phages and viruses),
as a Northern hybridization (RNA detection),
as serum analysis (e.g. cell type analysis of cells in serum by slot-blot analysis),
after amplification (e.g. PCR technique).
The invention therefore includes a method for the detection of nucleic acids which code for an ISL protein which is characterized in that the sample to be examined is incubated with a nucleic acid probe which is selected from the group comprising
a) the DNA sequences shown in SEQ ID NO:1 and SEQ ID NO:3 or a complementary sequence to these,
b) nucleic acids which hybridize under stringent conditions with one of the sequences from a),
the nucleic acid probe is incubated with the nucleic acid from the sample and the hybridization of the nucleic acid in the sample and nucleic acid probe is detected, if desired, via a further binding partner.
Thus, ISL is a valuable prognostic marker in viral, benign and malignant disease diagnostics.
Surprisingly, it was found that according to the invention it is not necessary to use an ISL polypeptide or nucleic acid directly for inhibition of the replication of viruses. It is also possible to use substances which induce production of ISL in cells. Such cells preferably are human blood lymphocytes, especially CD8+ cells. For induction of ISL production said cells are incubated, in vivo or in vitro, with such activating substances. If activation is performed in vitro the cells are subsequently administered to the patient, e.g., according to the above-mentioned U.S. Pat. No. 5,399,346. According to the invention it is easily possible to identify such substances which activate ISL production.
It has been found that such substances are, e.g., phytohaemagglutinin (PHA), Concanavalin A (ConA), histamine, polypeptides or nucleic acid molecules. Nucleic acid molecules are used as vectors which contain further elements securing expression of said nucleic acid molecules in the target cells. Said elements are known in the state of the art (e.g., regulatory sequences, promoter and/or operator regions). Suitable target cells for transfection with such nucleic acid molecules are preferably human cells, most preferably human blood cells such as lymphocytes, especially CD8+ cells.
Therefore, a further subject-matter of the invention is a method for the identification and production of a substance and a therapeutic agent for inhibition of the replication of viruses in a patient. Said method comprises combining with a pharmaceutically acceptable carrier a therapeutically effective amount of a substance which activates expression of a protein with ISL activity in CD8+ cells preferably in vivo. The protein the expression of which is activated is preferably a protein with the amino acid sequence shown in SEQ ID NO:2. A suitable substance can be identified in an assay (substance assay) wherein
a) PBMC from healthy blood donors are isolated by Ficoll-gradient separation;
b) CD8+ cells are isolated by magnetic cell sorting;
c) the purity of the preparation is tested by FACS analysis;
d) the preparation should have a content of approximately 95% CD8+ cells and 5% non-CD8+ contaminants to ensure adequate stimulation of CD8+ cells;
e) the substance to be tested for induction of expression of ISL activity is added to the cell culture in a concentration range of 1 pM to 10 mM;
i) IL-2 is added to the cell culture (180 U/ml cell culture medium) or to the culture of the transfected cells if the substance is a nucleic acid molecule;
g) after three days medium is completely removed and cells are cultured with IL-2 (180 U/ml cell culture medium) for three days;
h) cell culture supernatant is centrifuged (xc3x971000) to remove cells, sterile filtered, and aliquoted;
and further investigated in the above-mentioned HIV inhibition assay, whereby
i) CD8+-depleted PBMC are incubated with 50 xcexcl of said cell culture supernatants/1.5xc3x97106 cells in 150 xcexcl medium for half a hour at 37xc2x0 C.;
k) said CD8+-depleted PBMC are subsequently infected with HIV-1, preferably with HIV-1SF2, by incubating 1.5xc3x97106 cells in 150 xcexcl with 50 xcexcl HIV-1 stock solution containing 50 tissue infectious doses 50 (TCID50) for 1 h at 37xc2x0 C.;
l) said infected CD8+-depleted PBMC are washed to remove unbound HIV-1;
m) CD8+-depleted PBMC are cultivated at 37xc2x0 C. in a 5% CO2 atmosphere and medium and said cell culture supernatant is replaced after 3, 6, 9, and 12 days;
n) the amount of HIV-1 in the CD8+-depleted PBMC cell culture supernatants is determined at days 9 and 12 post infection by serially threefold dilutions of supernatant and inoculation in quadruplicate wells onto 2000 cells in 150 xcexcl medium of a highly susceptible indicator cell line, which must be routinely infectable to an extent of 85% or greater with said HIV-1 strains, e.g. the human HTLV-transformed lymphoma cell line MT4;
o) virus replication in each well is determined 8 days post infection by determination of the reverse transcriptase (RT) in the cell culture supernatant (reverse Transcriptase Assay, Boehringer Mannheim GmbH, Biochemica, 68298 Mannheim, Germany, Order No.: 1468 120) of every single well following the instructions of the manufacturer;
p) the tissue culture infectious doses 50 (TCID50) of the CD8+-depleted PBMC cultures is calculated following the method published by Karber (Karber, G. 1931. Assay for statistical analysis of pharmacological experiments. Arch. Exper. Path. V. Pharmakol. 162, 148 according to the formula:
log TCID50=Lxe2x88x92d(sxe2x88x920.5),
wherein
L=log of the lowest virus dilution
d=log of virus dilution
s=sum of virus-positive cell cultures;
q) inhibition of HIV-1 replication in the CD8+-depleted PBMC cultures is calculated by comparison of virus content of cell culture supernatants in an assay according to steps i) to p) and the virus content of an assay according to steps i) to p) where the cell culture supernatant to be tested for inhibition of HIV replication is replaced by normal medium (untreated control);
r) inhibition is found if the amount of viral replication in CD8+-depleted PBMC is inhibited in such a way that the amount of virus is only about 50%, more preferably 10%, most preferably 1% or less in comparison to the untreated control.
A further subject-matter of the invention is a therapeutic composition useful in treating a pathological condition characterized by excessive viral replication, especially retroviral replication, comprising at least a substance which activates ISL activity in CD8+ T cells, and which is characterized by the properties of the above-mentioned substance assay and HIV inhibition assay, and a pharmaceutically acceptable carrier.
Such a substance, which is obtainable and characterized by the above-mentioned substance assay, is useful for the induction and/or activation of ISL in mammalian cells, for the inhibition of the replication of viruses, preferably retroviruses, especially HIV and/or HTLV, for therapeutic treatment of benign and malignant diseases and viral, preferably retroviral, especially HIV and/or HTLV, infections.
It is also particularly preferred to use said substances for therapeutic treatment of such viral infections as soon as possible after the infection, preferably as soon as possible after the first virus peak.
The following examples, sequence listing, and figures are provided to aid the understanding of the present invention, the true scope of which is set forth in the appended claims. It is understood that modifications can be made in the procedures set forth without departing from the spirit of the invention.